Merge from BcdRNAi branch

Mainly whitespace changes, but a handful of feature changes (like lots
of filtering options on the MakeSummaryTable)
Treeview stuff from BcdRNAi
Merge branch 'BcdRNAi' into nextera

Conflicts:
	MakeSummaryTable.py
yet another new format for read files

this time its just the index sewuence, buried in basically arbitrary
directories. So fine. Fuck you, but I made it work.
Imorove Makefile to follow dependencies

there were some things i had been doing implicitly, which meant thr
build didnt actually work
Merge branch 'master' into nextera
Merge branch 'nextera' into HbRNAi
Cleaner printing of non-successful states in MST

before would print summary statistics of every library, now only prints
if it fails to match filter.  Also a bit more readable.
Track MapTable properly in Makefile
More tolerant of poor mapping

Note to self: I should spend some time tracking down why this isn't
working well.  Later.
Add startswith and contains lambdas to Utils.py
Add hatching as optional in SVG_heatmap
Merge branch 'HbRNAi'